Assays

Extracellular metabolites in T. brucei at different stage of cell growth have been quantified absolutely by isotope ratio based MS technique using uniformly 13C-labelled E. coli extract. This is the case study for method development of absolute quantification for metabolic flux analysis.

Intracellular metabolites in T. brucei at different stage of cell growth have been quantified absolutely by isotope ratio based MS technique using uniformly 13C-labelled E. coli extract. This is the case study for method development of absolute quantification for metabolic flux analysis.

Kinetic characterisation and mathematical modelling of LDH.

Links to additional gitlab repositories

"LINTUL simulates potential growth of a crop, i.e. its dry matter accumulation under ample supply of water and nutrients in a pest-, disease- and weed-free environment, under the prevailing weather conditions. The rate of dry matter accumulation is a function of irradiation and crop characteristics. The model makes use of the common observation that the crop growth rate under favourable conditions is proportional to the amount of light intercepted (Monteith, 1977). Dry matter production is, ...

This is a verified version of the model named  LINTUL in this repository. The model is verified against the benchmark FST implmmentation. LINTUL assumes non-limiting conditions. See the "LINTUL" model entry in this repository for a description

Originally submitted to PLaSMo on 2011-02-23 00:08:23

Lipidomic analysis by UPC2-MS of tissue samples from the GSF1 feed-switch experiment. Samples were analyzed at NTNU by Zdenka Bartosova and Per Bruheim.

There are three separate data files of lipid analysis in muscle, liver and gut tissue samples. Excel sheets contains both raw and normalised data of compounds abundance. Normalization to all compounds was used as a normalization method.

Columns: Compound 0.93_858.7669n Anova (p) 0,044998264 q Value 0,009417222 Max Fold Change 1,644961431 Maximum ...

Results from lipidomics analyses performed in cod liver microsomes of cod exposed to PAH and PFAS mixtures.

Km values of pyruvate kinase of different organisms without/with allosteric effector molecules collected from literature.

1. Preparation of B. subtilis cultures

Inoculate cells from -80°C stocks in 10 ml time-lapse microscopy (TLM) medium (62 mM K2HPO4 , 44mM KH2PO4, 15 mM (NH4)2SO4, 6.5 mM sodium citrate, 0.8 mM MgSO4, 0.02 % casamino acids, 27.8 mM glucose, 0.1 mM L-tryptophan, the pH was set to 7 using a KOH solution) supplemented with antibiotics, if necessary. Grow the cells overnight in a shake flask (30°C, 225 rpm). The following morning, dilute the cells 1:10 in pre-warmed chemically defined medium (CDM) (62 ...

Gene expression of cyp1a and acox1 measured by qPCR in liver of Atlantic cod exposed to PAHs and PFASs

RNA-seq data for In vivo 7 samples. Only 32 RNA samples from liver of male fish sequenced. Illumina poly(A)-RNA sequencing at UiB GCF, as in Yadetie et al., 2018.

Data for local pH monitoring expreiments for the dissolution part in publication: Microbial-induced calcium carbonate precipitation: An experimental toolbox for in situ and real-time investigation of micro-scale pH evolution. Included is data for the calibration, and from the dissolution experiment (Channel 1 data (signal from dye SR101) Channel 3 data (sigenl from dye R6G-EDA, and Channel 5 data (brightfield data)). Resolution is 512x512 pixel, images are recorded every 10sec. Data collection ...

Data for local pH monitoring precipitation experiments in publication: Microbial-induced calcium carbonate precipitation An experimental toolbox for in situ and real-time investigation of micro-scale pH evolution. Included are the calibration data, the signal from Channel 1 (representing signal from dye SR101) and Channel 3 (representing signal from pH dye R6G-EDA) and Channel 5 (brightfield images). Resolution is 512x512 pixel, images are recorded every 15 seconds. Data collection startet ...

This version is derived from a model from the article: Extension of a genetic network model by iterative experimentation and mathematical analysis. Locke JC, Southern MM, Kozma-Bognár L, Hibberd V, Brown PE, Turner MS, Millar AJ Mol. Syst. Biol. 2005; 1: 2005.0013 16729048,  SBML model of the interlocked feedback loop network The model describes the circuit depicted in Fig. 4 and reproduces the simulations in Figure 5A and 5B. It provides initial conditions, parameter values and rules for the ...

This is a version derived from a model from the article: Experimental validation of a predicted feedback loop in the multi-oscillator clock of Arabidopsis thaliana. Locke JC, Kozma-Bognár L, Gould PD, Fehér B, Kevei E, Nagy F, Turner MS, Hall A, Millar AJ Mol. Syst. Biol.2006;Volume:2;Page:59 17102804,   The model describes a three loop circuit of the Arabidopsis circadian clock. It provides initial conditions, parameter values and reactions for the production rates of the following species: LHY ...